rework error handling

cg_lims/EPPs/files/xml_to_udf.py

@@ -69,7 +69,9 @@ def get_run_parameters(process: Process) -> str:
     """Return RunParameters-file from location on the server."""
     flow_cell_id: str = get_flow_cell_id(process=process)
     return max(
-        glob.glob(f"/home/gls/hiseq_data/novaseq-clinical-preproc/*{flow_cell_id}/RunParameters.xml"),
+        glob.glob(
+            f"/home/gls/hiseq_data/novaseq-clinical-preproc/*{flow_cell_id}/RunParameters.xml"
+        ),
         key=os.path.getctime,
     )
 

cg_lims/EPPs/udf/calculate/qpcr_concentration.py

@@ -2,7 +2,7 @@
 import sys
 from pathlib import Path
 from statistics import mean
-from typing import Dict, List, Optional
+from typing import Dict, List, Optional, Tuple
 
 import click
 import numpy as np
@@ -12,6 +12,7 @@
 from cg_lims.exceptions import FailingQCError, LimsError, MissingFileError, MissingValueError
 from cg_lims.get.artifacts import get_artifact_by_name, get_artifacts
 from cg_lims.get.files import get_file_path
+from cg_lims.get.samples import get_one_sample_from_artifact
 from genologics.entities import Artifact, Process
 
 LOG = logging.getLogger(__name__)
@@ -146,12 +147,12 @@ def qpcr_concentration(
             summary_file=file_path
         )
         failed_samples: int = 0
+        missing_samples: List[Tuple[str, str]] = []
         for artifact in artifacts:
             artifact_well: str = artifact.location[1]
             if artifact_well not in quantification_data.keys():
-                raise MissingValueError(
-                    f"No values found for well {artifact_well} in the result file! "
-                    f"Please double check if sample {artifact.samples[0].id} has been placed correctly."
+                missing_samples.append(
+                    (get_one_sample_from_artifact(artifact=artifact).id, artifact_well)
                 )
             well_results: WellValues = quantification_data[artifact.location[1]]
             well_results.connect_artifact(artifact=artifact)
@@ -163,6 +164,12 @@ def qpcr_concentration(
             if well_results.artifact.qc_flag == "FAILED":
                 failed_samples += 1
 
+        if missing_samples:
+            raise MissingValueError(
+                f"No values found for the following samples in the result file! "
+                f"Please double check if the samples {missing_samples} have been placed correctly."
+            )
+
         if failed_samples:
             error_message: str = (
                 f" {failed_samples} sample(s) failed the QC! See the logs for further information."